RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ofc2wQ/RM_3314653.MonMay81449532023 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1683582592 Database = /dev/shm/rModeler.ofc2wQ/GCA_026979565.1_bVidCha1_merged_haplotype - Sequences = 178 - Bases = 1080457469 - N50 = 73120142 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 143328491-153566144 | [ 1 ] 133090838-143328490 | [ ] 122853186-133090838 | [ ] 112615533-122853185 | [ 2 ] 102377880-112615532 | [ ] 92140228-102377880 | [ ] 81902575-92140227 | [ ] 71664922-81902574 | [ 3 ] 61427270-71664922 | [ 1 ] 51189617-61427269 | [ ] 40951964-51189616 | [ ] 30714312-40951964 | [ 3 ] 20476659-30714311 |* [ 4 ] 10239006-20476658 |** [ 8 ] 1354-10239006 |************************************************** [ 156 ] Storage Throughput = good ( 906.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014922 bp ( 40011048 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:26 (hh:mm:ss) Elapsed Time Round Time: 00:18:14 (hh:mm:ss) Elapsed Time : 125 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2412 repeats masked totaling 596656 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022240 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10021540 bp After Masking: 9195603 bp Masked: 8.24 % -- Input Database Coverage: 10022240 bp out of 1080457469 bp ( 0.93 % ) Sampling Time: 00:01:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:12:23 (hh:mm:ss) Elapsed Time, 1379 HSPs Collected Number of families returned by RECON: 274 Round Time: 00:13:38 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7881 repeats masked totaling 1999139 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032761 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 30029587 bp After Masking: 27388886 bp Masked: 8.79 % -- Input Database Coverage: 40055001 bp out of 1080457469 bp ( 3.71 % ) Sampling Time: 00:03:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:54:11 (hh:mm:ss) Elapsed Time, 12221 HSPs Collected Number of families returned by RECON: 1821 Round Time: 00:59:15 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24812 repeats masked totaling 6618811 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90048862 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 90031674 bp After Masking: 81227306 bp Masked: 9.78 % -- Input Database Coverage: 130103863 bp out of 1080457469 bp ( 12.04 % ) Sampling Time: 00:08:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 04:46:09 (hh:mm:ss) Elapsed Time, 52590 HSPs Collected Number of families returned by RECON: 11249 Round Time: 05:03:25 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 82348 repeats masked totaling 22562577 bp(s). - TE Masking time 00:02:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270045533 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 270004916 bp After Masking: 241208631 bp Masked: 10.67 % -- Input Database Coverage: 400149396 bp out of 1080457469 bp ( 37.04 % ) Sampling Time: 00:27:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22940151 Comparison Time: 30:35:48 (hh:mm:ss) Elapsed Time, 266315 HSPs Collected Number of families returned by RECON: 75284 Round Time: 31:54:58 (hh:mm:ss) Elapsed Time : 262 families discovered. RepeatScout/RECON discovery complete: 485 families found Classification Time: 00:27:00 (hh:mm:ss) Elapsed Time Program Time: 38:56:30 (hh:mm:ss) Elapsed Time